Genome-wide identification and gene expression analysis of the 14–3-3 gene family in potato (Solanum tuberosum L.)

Abstract

Background 14–3-3 proteins are essential in regulating various biological processes and abiotic stress responses in plants. Although 14–3-3 proteins have been studied in model plants such as Arabidopsis thaliana and Oryza sativa, there is a lack of research on the 14–3-3 gene family in potatoes (Solanum tuberosum L.). Results A total of 18 14–3-3 genes encoding proteins containing a typical conserved PF00244 domain were identified by genome-wide analysis in potatoes. The St14–3-3 gene family members were unevenly distributed across the chromosomes, and gene structure analysis showed that gene length and intron number varied greatly among the members. Phylogenetic analysis of 14–3-3 proteins in potatoes and other plant species showed that they could be divided into two distinct groups (ε and non-ε). Members in the ε group tended to have similar exon-intron structures and conserved motif patterns. Promoter sequence analysis showed that the St14–3-3 gene promoters contained multiple hormone-, stress-, and light-responsive cis-regulatory elements. Synteny analysis suggested that segmental duplication events contributed to the expansion of the St14–3-3 gene family in potatoes. The observed syntenic relationships between some 14–3-3 genes from potato, Arabidopsis, and tomato suggest that they evolved from a common ancestor. RNA-seq data showed that St14–3-3 genes were expressed in all tissues of potatoes but that their expression patterns were different. qRT-PCR assays revealed that the expression levels of nearly all tested St14–3-3 genes were affected by drought, salt, and low-temperature stresses and that different St14–3-3 genes had different responses to these stresses. Conclusions In summary, genome-wide identification, evolutionary, and expression analyses of the 14–3-3 gene family in potato were conducted. These results provide important information for further studies on the function and regulation of St14–3-3 gene family members in potatoes.

Phylogenetic and Expression Analysis of the Sucrose Synthase and Sucrose Phosphate Synthase Gene Family in Potatoes

“…The doubled monoploid S. phureja DM1-3 516 R44 (DM) reference genome has been updated with the development of high-throughput sequencing technology [ 20 , 21 ]. In recent years, several tetraploid potato genomes have been sequenced [ 22 , 23 ], and a large number of functional genes and their gene family members have been reported [ 24 , 25 , 26 , 27 ]. SUSs and SPSs play crucial roles in sucrose metabolism in plants, but a comprehensive analysis of StSUS and StSPS gene families in potatoes is still lacking.…”

Genome-Wide Identification and Characterization of the Sweet Orange (Citrus sinensis) GATA Family Reveals a Role for CsGATA12 as a Regulator of Citrus Bacterial Canker Resistance

“…Furthermore, based on the conserved domains, Arabidopsis thaliana B-GATA proteins can be further subclassified into the N-terminal HAN domain and Cterminal LLM domain [4]. To date, many GATA gene family members have been classified by systematic annotation, such as 30,28,64,28,30,96,31,49, and 79 members of the GATA members have been annotated in Arabidopsis [5], rice [6], soybean [7], millet [3], tomato [1], rapeseed [8], Phyllostachys pubescens [9], potato [10], and wheat [11], respectively. These gene families offer a valuable reference to further explore the biological characteristics and functions of members of this GATA transcription factor family.…”